Fig. 2

Comparison of TRN transfer methods. The plots show the PR-AUC of bidirectional transfers between 179 TF-specific species pairs using motif-based (direct transfer, direct discovery with true intergenic and direct discovery with random intergenic) and transfer-based methods (ortholog, COG and interaction modes), as well as a mixed model integrating direct transfer and the union of all network-based transfer methods. The results obtained with a permutation of the target motif are shown for comparison. The x-axis denotes protein similarity as the BLOSUM62 score of the ungapped pair-wise alignment between reference and target TF protein sequences. PR-AUC values are normalized to the respective AUC of the known target TF-binding motif to compensate for the decreased search efficiency of low information content motifs. Spearman correlation coefficients (ρ) of PR-AUC with protein similarity are shown for each case